Online Supplementary Material

This page contains supplementary data files for

RNAcode: robust prediction of protein coding regions in comparative genomics data
Stefan Washietl, Sven Findeiß, Stephan Müller, Stefan Kalkhof, Martin von Bergen, Ivo L. Hofacker, Peter F. Stadler & Nick Goldman

All data sets

All data sets in one package: all.tar.gz (6.5 MB)

Benchmark test sets

Positive (true coding) and negative (non-coding) alignments in UCSC MAF format for all test sets:

E. coli screen

Genome wide RNAcode predictions:

GTF: ecoli_0.05.gtf
UCSC compatible BED format*: ecoli_0.05_ucsc.bed

35 short ORFs extended from intergenic RNAcode predictions:

BED: ecoli_35_short_ORFs.bed
BED (UCSC coordinates)*: ecoli_35_short_ORFs_ucsc.bed
Multiple fasta (nucleotide): ecoli_35_short_ORFs.fa
Multiple fasta (amino acids): ecoli_35_short_ORFs.faa

*Coordinates BED files are adjusted to UCSC conventions (position in the second column = genomic position - 1) and can be loaded as "Custom Track" into the UCSC genome browser:
http://archaea.ucsc.edu/cgi-bin/hgTracks?&clade=bacteria-gammaproteobacteria&org=Escherichia+coli+K12&db=eschColi_K12